Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications

BackgroundParasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control.MethodsUsing a combination of three genes (COI,28S, andCAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset.ResultsThe monophyly of the tribe Euphorini and the two generaPeristenusandLeiophronwere confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications ofLeiophron sensu latowere not supported, and the monotypic genusMamawas also not supported.DiscussionEuphoriella,Euphoriana,Euphorus, andMamasyn. n,have been synonymized underLeiophron. Mama mariaesyn. nwas placed as a junior synonym ofLeiophron reclinator. The generic concepts ofPeristenusandLeiophronwere refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe.

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Phylogenetic relationships of the family Gryporhynchidae (Cestoda: Cyclophyllidea) inferred through SSU and LSU rDNA sequences

Journal of Helminthology ◽

10.1017/s0022149x18000846 ◽

2018 ◽

Vol 93 (6) ◽

pp. 763-771 ◽

Cited By ~ 1

Author(s):

M.P. Ortega-Olivares ◽

M. García-Varela

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Species Composition ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Lsu Rdna ◽

Rdna Sequences ◽

The Family ◽

Shape And Size

AbstractTapeworms of the family Gryporhynchidae are endoparasites of fish-eating birds distributed worldwide. Currently the family contains 16 genera classified on the basis of the morphology of the rostellar apparatus, rostellar hooks and strobilar anatomy. However, the phylogenetic relationships among the genera are still unknown. In this study, sequences of the near complete 18S (SSU) and 28S (LSU) from rDNA of 13 species of gryporhynchids (adult specimens) representing eight genera (Cyclustera, Dendrouterina, Glossocercus, Gryporhynchidae gen. sp., Neovalipora, Paradilepis, Parvitaenia, Valipora) and one species of metacestode from fish (Neovalipora) were generated. Additionally, sequences of metacestodes of the genera Amirthalingamia, Neogryporhynchus, Paradilepis, Parvitaenia and Valipora from Africa recently added to the GenBank database were analysed. Phylogenetic relationships were inferred using maximum-likelihood (ML) and Bayesian inference of each (SSU and LSU) dataset. The phylogenetic analyses indicated that the family Gryporhynchidae is a well-supported monophyletic group within the Cyclophyllidea. The trees inferred with SSU and LSU datasets had similar topologies and suggested that the genera Glossocercus (two species sequenced) and Paradilepis (four spp.) are monophyletic. In contrast, Dendrouterina, Parvitaenia and Valipora are paraphyletic, suggesting that the species composition of these genera should be critically reviewed. Interestingly, species of the genera that use the same groups of definitive hosts such as herons (Ardeidae), cormorants (Phalacrocoracidae) and ibis (Threskiornithidae) are together in the phylogenetic tree, even though they differ markedly from each other in some morphological characters, especially shape and size of rostellar hooks.

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Gloeodontia yunnanensis sp. nov. (Russulales, Basidiomycota) from China, evidenced by morphological characters and phylogenetic analyses

Phytotaxa ◽

10.11646/phytotaxa.432.2.1 ◽

2020 ◽

Vol 432 (2) ◽

pp. 111-118

Author(s):

LU CHEN ◽

ZHENG-JUN SHI ◽

CHUN-HUA WU ◽

CHANG-LIN ZHAO

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Strong Support ◽

Morphological Characters ◽

Fungal Species ◽

Monophyletic Lineage ◽

Thin Walled ◽

Inference Methods

A new wood-inhabiting fungal species, Gloeodontia yunnanensis, is proposed based on a combination of morphological features and DNA data. The species is characterized by an annual, resupinate basidiomata with smooth hymenial surface, a monomitic hyphal system with thin-walled, clamped generative hyphae and obclavate cystidia and subglobose to globose, hyaline, thick-walled, asperulate, strongly amyloid, acyanophilous basidiospores measuring 3.3–4.3 × 2.5–3.5 µm. Sequences of ITS and 28S gene regions of the studied samples were generated and phylogenetic analyses were performed with Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The analyses based on ITS+28S sequences showed that G. yunnanensis nested in the Gloeodontia clade and formed a monophyletic lineage with strong support (100% BS, 100% BP, 1.00 BPP).

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Morpho-molecular diversity of Linocarpaceae (Chaetosphaeriales): Claviformispora gen. nov. from decaying branches of Phyllostachys heteroclada

MycoKeys ◽

10.3897/mycokeys.69.54231 ◽

2020 ◽

Vol 69 ◽

pp. 113-129

Author(s):

Xiu-Lan Xu ◽

Chun-Lin Yang ◽

Rajesh Jeewon ◽

Dhanushka N. Wanasinghe ◽

Ying-Gao Liu ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Molecular Diversity ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

New Taxon ◽

Dna Sequence Data ◽

Distinct Genus

In this paper, Claviformisporagen. nov. in Linocarpaceae is introduced from Phyllostachys heteroclada in Sichuan Province, China. The new genus is characterised by its distinct morphological characters, such as ostiole with periphyses, asci with a thick doughnut-shaped, J- apical ring and clavate ascospore without septum-like band and appendage. Maximum Likelihood and Bayesian Inference phylogenetic analyses, based on DNA sequence data from ITS, LSU, SSU and TEF-1α regions, provide further evidence that the fungus is a distinct genus within this family. The new genus is compared with similar genera, such as Linocarpon and Neolinocarpon. Descriptions, illustrations and notes are provided for the new taxon.

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PHYLOGENY, BIOGEOGRAPHY AND CHARACTER EVOLUTION OF DORSTENIA (MORACEAE)

Edinburgh Journal of Botany ◽

10.1017/s096042861200025x ◽

2012 ◽

Vol 69 (3) ◽

pp. 413-440 ◽

Cited By ~ 7

Author(s):

T. M. Misiewicz ◽

N. C. Zerega

Keyword(s):

Maximum Likelihood ◽

Life Form ◽

Sequence Data ◽

Morphological Characters ◽

Molecular Dating ◽

Its Sequence ◽

The Family ◽

Storage Organs ◽

Woody Habit ◽

Origin Hypothesis

Dorstenia, the second largest genus (105 species) within the Moraceae, is the only genus in the family with woody, herbaceous and succulent species. All but one species of Dorstenia are restricted to the Neotropics or Africa, and it is the only genus in the family with an almost equal transatlantic distribution. This work presents the first molecular phylogeny and the first evolutionary study to examine origin and diversification within the genus. We inferred the phylogeny with ITS sequence data using Bayesian and maximum likelihood approaches. We tracked the evolution of distinct morphological characters and tested for correlated evolution in multiple characters. Time and place of Dorstenia’s origin were estimated to test a post-Gondwanan versus a Gondwanan origin hypothesis using fossil calibrations, Bayesian molecular dating, and maximum likelihood-based ancestral range reconstructions. Our phylogenetic analysis supports the monophyly of Dorstenia; previous subgeneric classifications are polyphyletic and must be re-evaluated. Woody habit, phanerophytic life form, macrospermy, and lack of storage organs are ancestral traits found in African Dorstenia. Evolution of woodiness and macrospermy are correlated. Dorstenia appears to have originated in Africa, radiated into the Neotropics and subsequently re-colonised Africa. Whether or not the extant distribution is the result of vicariance or dispersal is equivocal.

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New species of Mycena (Mycenaceae, Agaricales) with colored lamellae and three new species records from China

Phytotaxa ◽

10.11646/phytotaxa.361.3.2 ◽

2018 ◽

Vol 361 (3) ◽

pp. 266 ◽

Cited By ~ 2

Author(s):

QIN NA ◽

TOLGOR BAU

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Bayesian Inference ◽

Maximum Likelihood ◽

North America ◽

Morphological Characters ◽

Its Sequences ◽

Monophyletic Clade ◽

Three New Species ◽

First Time

Four species of Mycena possessing a colored lamellar are reported. Of these, Mycena entolomoides is described as new and is distinguished by an incarnate color of the whole lamellae, and M. citrinomarginata, M. purpureofusca, and M. strobilinoidea are recorded for the first time in China. A complete description, drawings and photographs of the morphological characters of M. entolomoides sp. nov. are accompanied by comparisons with closely related taxa. The three species newly recorded in China are considered in agreement with those species in Europe and North America. Phylogenetic analysis based on ITS sequences showed that M. entolomoides sp. nov. forms a monophyletic clade, well supported by maximum likelihood and Bayesian inference.

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Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data

Neotropical Ichthyology ◽

10.1590/1982-0224-20180016 ◽

2018 ◽

Vol 16 (3) ◽

Cited By ~ 4

Author(s):

Dahiana Arcila ◽

Paulo Petry ◽

Guillermo Ortí

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

South America ◽

Sister Group ◽

The Other ◽

Molecular Analyses ◽

Mitochondrial Data ◽

The Family ◽

Commercially Important ◽

Group Relationships

ABSTRACT Characiformes is an order of freshwater fishes that includes many commercially important and emblematic species from South America and Africa, such as the popular piranhas, hatchetfishes, African tiger fishes and tetras. The order is split into two suborders with a total of 24 families, 282 genera and ca. 2,100 species. Here, we present an expanded phylogeny of characiform fishes, including data for 520 species and three genes (12S, 16S and RAG1), and the recently described family Tarumaniidae, which has not been examined by previous molecular analysis. Although our genetic coverage is limited to three gene fragments, the tree inferred based on maximum likelihood and Bayesian inference supports the monophyly of all characiform families and is largely congruent with results from recent studies that sampled less taxa but more genes. Also in agreement with a morphological hypothesis, our results strongly support the sister-group relationships between the family Tarumaniidae and Erythrinidae. Based on our results and that of the other molecular analyses, we propose a revised circumscription of the superfamily Erythrinoidea to include the families Tarumaniidae and Erythrinidae only.

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An investigation of irreproducibility in maximum likelihood phylogenetic inference

Nature Communications ◽

10.1038/s41467-020-20005-6 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Xing-Xing Shen ◽

Yuanning Li ◽

Chris Todd Hittinger ◽

Xue-xin Chen ◽

Antonis Rokas

Keyword(s):

Maximum Likelihood ◽

Phylogenetic Trees ◽

Single Gene ◽

Phylogenetic Inference ◽

Gene Trees ◽

Seed Number ◽

Substitution Model ◽

Individual Gene ◽

Considerable Fraction ◽

Log Files

AbstractPhylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates (Run1 and Run2) for each of 19,414 gene alignments in 15 animal, plant, and fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and Run2 sets of individual gene trees are topologically irreproducible for 9/15 phylogenomic datasets, whereas concatenation-based phylogenies inferred twice from the same supermatrix are reproducible. Our simulations further show that irreproducible phylogenies are more likely to be incorrect than reproducible phylogenies. These results suggest that a considerable fraction of single-gene ML trees may be irreproducible. Increasing reproducibility in ML inference will benefit from providing analyses’ log files, which contain typically reported parameters (e.g., program, substitution model, number of tree searches) but also typically unreported ones (e.g., random starting seed number, number of threads, processor type).

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Two new Xeromphalina (Mycenaceae, Agaricales) species with eccentric stipes from subtropical China

Phytotaxa ◽

10.11646/phytotaxa.379.4.1 ◽

2018 ◽

Vol 379 (4) ◽

pp. 277

Author(s):

LI-NA LIU ◽

TOLGOR BAU

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Internal Transcribed Spacer ◽

Growth Habit ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Subtropical China ◽

Pinus Densata ◽

Montane Zone ◽

Internal Transcribed Spacer Sequences

Two new Xeromphalina species with eccentric stipes are described from subtropical China. Xeromphalina brevipes sp. nov. is characterized by a pileus without a depressed centre, a rather short stipe, cylindrical basidiospores, and subcoralloid to coralloid circumcystidia and caulocystidia. Xeromphalina utricularis sp. nov. can be distinguished by its small and cylindrical basidiospores, utriform cystidia and its growth habit on rotten Pinus densata Mast. wood in the montane zone. Photographs and illustrations of the basidiomata and morphological features of these species are presented. Morphological characters, when compared with related Xeromphalina species, and phylogenetic analyses based on internal transcribed spacer sequences with Maximum Likelihood and Bayesian Inference, demonstrate that the two new taxa are different from related Xeromphalina species.

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Morpho-molecular diversity of Linocarpaceae (Chaetosphaeriales): Claviformispora gen. nov. from decaying branches of Phyllostachys heteroclada

MycoKeys ◽

10.3897/mycokeys.70.54231 ◽

2020 ◽

Vol 70 ◽

pp. 1-17

Author(s):

Xiu-Lan Xu ◽

Chun-Lin Yang ◽

Rajesh Jeewon ◽

Dhanushka N. Wanasinghe ◽

Ying-Gao Liu ◽

...

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Molecular Diversity ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

New Taxon ◽

Dna Sequence Data ◽

Distinct Genus

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A new species of the genus Euxaldar Fennah, 1978 (Hemiptera, Fulgoromorpha, Issidae) from China and revision on the molecular phylogeny of the family

ZooKeys ◽

10.3897/zookeys.1021.35510 ◽

2021 ◽

Vol 1021 ◽

pp. 19-35

Author(s):

Liang-Jing Yang ◽

Zhi-Min Chang ◽

Lin Yang ◽

Xiang-Sheng Chen

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Bayesian Inference ◽

Maximum Likelihood ◽

Molecular Phylogeny ◽

Molecular Phylogenetic Analysis ◽

The Family ◽

Molecular Phylogenetic ◽

First Time ◽

A New Species

A new species Euxaldar daweishanensis Yang, Chang & Chen, sp. nov. is described and illustrated from southwestern China. The female genitalia of the genus Euxaldar is described and presented for the first time. A checklist and key to the known species of the genus are provided. A revised molecular phylogenetic analysis of the family Issidae based on combined partial sequences of 18S, 28S, COI, and Cytb is provided using both Maximum likelihood and Bayesian inference analyses.

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